GEO DataSets

(Submitter supplied) Time-series of single-cell RNA-sequencing performed on stem cell derived retinal organoids or post-mortem tissue from the developing and adult retina

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: CSV, MTX

(Submitter supplied) Injury induces retinal Muller glia of non-mammalian, but not mammalian, vertebrates to generate neurons. To identify gene regulatory networks that control neurogenic competence in retinal glia, we used bulk and single-cell RNA-seq and ATAC-seq analysis to comprehensively profile gene expression and chromatin conformation in Muller glia from zebrafish, chick and mice. This was conducted during glial development, following inner and outer retinal injury, as well as following treatment with extrinsic factors that induce glial reprogramming. more...

Organism:

Danio rerio; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL19057 GPL20828

145 Samples

Download data: NARROWPEAK, XLSX

(Submitter supplied) The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: MTX, TSV

(Submitter supplied) The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: MTX, TSV

(Submitter supplied) Cis-regulatory elements (CREs) play a critical role in the development, maintenance, and disease-states of all human cell types. In the human retina, CREs have been implicated in a variety of inherited retinal disorders. To characterize cell-class-specific CREs in the human retina and elucidate their potential functions in development and disease, we performed single-nucleus (sn)ATAC-seq and snRNA-seq on the developing and adult human retina and on human retinal organoids. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24676

51 Samples

Download data: MTX, TSV

(Submitter supplied) Gene regulatory networks (GRNs), consisting of transcription factors and their target cis-regulatory sequences, control neurogenesis and cell fate specification in the developing central nervous system, but their organization is poorly characterized. In this study, we performed integrated scRNA-seq and scATAC-seq analysis from both mouse and human retina to profile dynamic changes in gene expression, chromatin accessibility and transcription factor footprinting during retinal neurogenesis and gliogenesis. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL19057

38 Samples

Download data: MTX, TXT

(Submitter supplied) Expressing HDAC5 mutant whose serine 259 and 488 have been replaced by alanine (HDAC5AA) promotes optic nerve regeneration in retinal ganglion cells. However, expressing GFP, HDAC5WT and HDAC5DAD, whose serine 259 and 498 have been replaced by aspartic acid and serine 280 by alanine, do not promote optic nerve regeneration. The goal of this experiment was to determine the underlying mechanisms leading to the phenotypical differences in optic nerve regeneration between control GFP, HDAC5DAD, and HDAC5AA by analyzing the retinal transcriptome of the different treatments.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

16 Samples

Download data: XLSX

(Submitter supplied) The failure of adult CNS neurons to survive and regenerate their axons after injury or in neurodegenerative disease remains a major target for basic and clinical neuroscience. Recent data demonstrated in the adult mouse that exogenous expression of Sry-related high-mobility-box 11 (Sox11) promotes optic nerve regeneration after optic nerve injury, but exacerbates the death of a subset of retinal ganglion cells, alpha-RGCs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Application of single-cell sequencing C1 to obtain neural retinal transcriptomes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

800 Samples

Download data: CSV

(Submitter supplied) Application of single-cell sequencing technology "10X" to obtain neural retinal transcriptomes. This resource highlight transcriptional sequences that establish the hierarchical ordering of early cell fate specification in the retina.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: CSV

(Submitter supplied) In this study, we performed RNA-seq of injured and FACS-purified RGCs receiving CRISPR-mediated knockout of ATF3, ATF4, CEBPγ or CHOP

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

21 Samples

Download data: TSV

(Submitter supplied) In this study, we profiled epigenetic and transcriptional landscapes in injured RGCs to identify transcription factors driving critical chromatin state and gene expression changes in reponse to injury.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

30 Samples

Download data: TSV, TXT

(Submitter supplied) We report the genome-wide RNA sequencing changes to isolated retinal ganglion cells (RGCs) from immunopanned embryonic day 18 (E18) and early postnatal (P5) wildtype mouse retinas. We report the transcriptomic change associated with RGCs in a survival and regenerative state, and use gene-set enrichment analysis (GSEA) to predict the upstream transcription factors likely regulating these observed changes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: CSV

(Submitter supplied) Background: The vertebrate retina consists of six major classes of neuronal cells. During development, these cells are generated from a pool of multipotent retinal progenitor cells (RPCs) that express the gene Vsx2. Fate-restricted RPCs have recently been identified, with limited mitotic potential and cell fate possibilities compared to multipotent RPCs. One population of fate-restricted RPCs, marked by activity of the regulatory element ThrbCRM1, gives rise to both cone photoreceptors and horizontal cells. more...

Organism:

Gallus gallus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19005

2 Samples

Download data: BIGWIG

(Submitter supplied) Single cell RNA sequencing using either an adapted Smart-seq2 protocol on Chx10-GFP (+) retinal progenitor cells; 10x Genomics Chromium Single Cell system across 10 timepoints of mouse retinal development to examine retinal progenitor cell heterogeneity across retinal development and global changes in gene expression from early retinal neuroepithelial cells through specification and differentiation of retinal cell types; 10X Genomics Chromium Single Cell on P14 Nfia/b/x het control or Nfia/b/x tCKO (Chx10-Cre-GFP) retinas

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

882 Samples

Download data: MTX, TSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL22396 GPL23945

12 Samples

Download data: BED, BIGWIG, TXT

(Submitter supplied) CNS neurons lose their ability to grow and regenerate axons during development. This is the case for Retinal Ganglion Cells (RGCs) in the retina, which transmit visual information to the brain via axons projecting into the optic nerve. RGCs are unable to regenerate their axon after injury, and start a degeneration process that leads to cell death and loss of vision. To identifying molecular mechanisms that increase regeneration of RGC and may offer new treatment strategies for patients with glaucoma or other types of optic neuropathies, we focused on the identification of transcription factors and chromatin accessible sites that are enriched in RGC during developmental stages, in which axon growth capacity is robust. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23945

8 Samples

Download data: TXT

(Submitter supplied) CNS neurons lose their ability to grow and regenerate axons during development. This is the case for Retinal Ganglion Cells (RGCs) in the retina, which transmit visual information to the brain via axons projecting into the optic nerve. RGCs are unable to regenerate their axon after injury, and start a degeneration process that leads to cell death and loss of vision. To identifying molecular mechanisms that increase regeneration of RGC and may offer new treatment strategies for patients with glaucoma or other types of optic neuropathies, we focused on the identification of transcription factors and chromatin accessible sites that are enriched in RGC during developmental stages, in which axon growth capacity is robust. more...

Organism:

Rattus norvegicus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22396

4 Samples

Download data: BED, BIGWIG

(Submitter supplied) The rapid improvements in single cell sequencing technologies and analyses methods afford greater scope for dissecting organoid cultures composed of multiple cell types and create an opportunity to interrogate these models to understand tissue biology, cellular behaviour and interactions. To this end, retinal organoids generated from human embryonic stem cells (hESCs) were analysed by single cell RNA-Sequencing at three time points of differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

79 Samples

Download data: CSV

(Submitter supplied) Purpose: The goals of this study are to identify the transcriptional profile of retinal ganglion cells (RGCs) with the capacity to regenerate an axon, and contrast this profile with the profile of RGCs that cannot regenerate an axon. Methods: See sample pages for protocols for tissue preparation, RNA extraction and purification, library construction and data processing. Results: RNA from the 12 samples was sequenced to an average depth of 42 million reads. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT